A B C D E F G H I J L M N O P Q R S T U V W X

G

get(String) - Method in class org.vivoweb.harvester.util.args.ArgList

Gets the value of the argument or default value if not set

getAll(String) - Method in class org.vivoweb.harvester.util.args.ArgList

Gets the values of the argument (excluding a default value)

getAll(String, boolean) - Method in class org.vivoweb.harvester.util.args.ArgList

Gets the values of the argument

getAppName() - Method in class org.vivoweb.harvester.util.args.ArgParser

Get the application name

getArgDefs() - Method in class org.vivoweb.harvester.util.args.ArgParser

Get the argument definitions

getBatchSize() - Method in class org.vivoweb.harvester.fetch.NIHFetch

getData() - Method in class org.vivoweb.harvester.util.repo.Record

Getter for Data

getDataSet() - Method in class org.vivoweb.harvester.util.repo.JenaConnect

Get the dataset for this connection Can be very expensive when using RDB connections (SDB, TDB, and Mem are fine)

getDataSet() - Method in class org.vivoweb.harvester.util.repo.RDBJenaConnect

getDataSet() - Method in class org.vivoweb.harvester.util.repo.SDBJenaConnect

getDataSet() - Method in class org.vivoweb.harvester.util.repo.TDBJenaConnect

getDate() - Method in class org.vivoweb.harvester.util.repo.RecordMetaData

Getter for date

getDbType() - Method in class org.vivoweb.harvester.util.repo.DBJenaConnect

Get the dbType for Jena

getDefaultValue() - Method in class org.vivoweb.harvester.util.args.ArgDef

Get the default value

getDescription() - Method in class org.vivoweb.harvester.util.args.ArgDef

Get the argument description

getEmailAddress() - Method in class org.vivoweb.harvester.fetch.NIHFetch

getEn() - Method in class org.vivoweb.harvester.util.IterableAdaptor

Accessor for en

getID() - Method in class org.vivoweb.harvester.util.repo.Record

Getter for ID

getJenaModel() - Method in class org.vivoweb.harvester.util.repo.JenaConnect

Accessor for Jena Model

getLastMetaData(String, RecordMetaData.RecordMetaDataType, Class<?>) - Method in class org.vivoweb.harvester.util.repo.RecordHandler

Get the last RecordMetaData of a given type by a given operator for a given record

getLatestRecord() - Method in class org.vivoweb.harvester.fetch.NIHFetch

Get latest NIH result

getLatestRecord() - Method in class org.vivoweb.harvester.fetch.NLMJournalFetch

getLatestRecord() - Method in class org.vivoweb.harvester.fetch.PubmedFetch

getLatestRecord() - Method in class org.vivoweb.harvester.fetch.PubmedHTTPFetch

getLongOption() - Method in class org.vivoweb.harvester.util.args.ArgDef

Get the long --Foo type option flag

getMaxRecords() - Method in class org.vivoweb.harvester.fetch.NIHFetch

getMD5() - Method in class org.vivoweb.harvester.util.repo.RecordMetaData

Getter for md5hash

getModelName() - Method in class org.vivoweb.harvester.util.repo.JenaConnect

Get the modelName

getOperation() - Method in class org.vivoweb.harvester.util.repo.RecordMetaData

Getter for operation

getOperator() - Method in class org.vivoweb.harvester.util.repo.RecordMetaData

Getter for operator

getOptions() - Method in class org.vivoweb.harvester.util.args.ArgParser

Get the Options

getOptMap() - Method in class org.vivoweb.harvester.util.args.ArgParser

Get the mapping of option flag to ArgDef

getOsWriter() - Method in class org.vivoweb.harvester.fetch.NIHFetch

getParam(Map<String, String>, String, boolean) - Method in class org.vivoweb.harvester.util.repo.RecordHandler

Get a specified parameter

getParameterDescription() - Method in class org.vivoweb.harvester.util.args.ArgDef

Get the description for this arguments parameter

getParser(String, String) - Static method in class org.vivoweb.harvester.fetch.NIHFetch

Get the ArgParser for this task

getParser() - Static method in class org.vivoweb.harvester.translate.GlozeTranslator

Get the ArgParser for this task

getRecord(String) - Method in class org.vivoweb.harvester.util.repo.RecordHandler

Get a record

getRecordData(String) - Method in class org.vivoweb.harvester.util.repo.JDBCRecordHandler

getRecordData(String) - Method in class org.vivoweb.harvester.util.repo.JenaRecordHandler

getRecordData(String) - Method in class org.vivoweb.harvester.util.repo.MapRecordHandler

getRecordData(String) - Method in class org.vivoweb.harvester.util.repo.RecordHandler

Retrieve the data for a given record

getRecordData(String) - Method in class org.vivoweb.harvester.util.repo.TextFileRecordHandler

getRecordMetaData(String) - Method in class org.vivoweb.harvester.util.repo.JDBCRecordHandler

getRecordMetaData(String) - Method in class org.vivoweb.harvester.util.repo.JenaRecordHandler

getRecordMetaData(String) - Method in class org.vivoweb.harvester.util.repo.MapRecordHandler

getRecordMetaData(String) - Method in class org.vivoweb.harvester.util.repo.RecordHandler

Retrieves all metadata for a given record

getRecordMetaData(String) - Method in class org.vivoweb.harvester.util.repo.TextFileRecordHandler

getSearchTerm() - Method in class org.vivoweb.harvester.fetch.NIHFetch

getShortOption() - Method in class org.vivoweb.harvester.util.args.ArgDef

Get the short -X type option flag

getToolName() - Method in class org.vivoweb.harvester.fetch.NIHFetch

getTypoDamerauLevenshtein(CharSequence, CharSequence, Map<Character, Map<Character, Float>>) - Static method in class org.vivoweb.harvester.score.algorithm.NormalizedTypoDifference

Typo-Accounting Modified Damerau-Levenshtein Distance

getUnusedURI(String, JenaConnect...) - Static method in class org.vivoweb.harvester.qualify.ChangeNamespace

Gets an unused URI in the the given namespace for the given models

getURLContents(String) - Static method in class org.vivoweb.harvester.util.WebHelper

Get the contents of a url

getUsage() - Method in class org.vivoweb.harvester.util.args.ArgParser

Get the usage message for this arg list

getValueMap(String) - Method in class org.vivoweb.harvester.util.args.ArgList

Gets the value map for the argument

getXPathResult(String, String) - Static method in class org.vivoweb.harvester.util.XPathTool

Export xpath selection from xml file

GlozeTranslator - Class in org.vivoweb.harvester.translate

Gloze Tranlator This class translates XML into its own natural RDF ontology using the gloze library.

GlozeTranslator() - Constructor for class org.vivoweb.harvester.translate.GlozeTranslator

Default Constructor

GlozeTranslator(String...) - Constructor for class org.vivoweb.harvester.translate.GlozeTranslator

Constructor

GlozeTranslator(ArgList) - Constructor for class org.vivoweb.harvester.translate.GlozeTranslator